Virome characterization of pome fruit European genetic resources for future breeding and risk analysis

Pome fruit viruses associated with economically important pome fruit diseases have been thoroughly studied and characterized over the years, mainly focused on commercial cultivars. Nevertheless, behind commercial cultivars there is a significant genetic diversity preserved in genetic resources collections. Germplasm is not only important for the conservation of plant genetic diversity but also as a source of genetic material and new traits for breeding and for direct use for food and agriculture.
The project aims at conducting a large-scale survey of apple (Malus Mill.) and pear (Pyrus L.) from important ex-situ European genetic resources collections to characterize their Virome. The samples will finally come from at least four different countries (Belgium, France, Switzerland and Slovenia). High-throughput sequencing techniques and bioinformatics tools are used to reconstruct the genome of the present viruses and perform further phylogenetic analyses.
The proof of concept trial of five apple and five pear samples led to the first detection in Belgium of apple luteovirus 1, apple rubodvirus 1 and apple hammerhead viroid-like circular RNA. Other detected viruses previously reported in Belgium are apple stem pitting virus, apple stem grooving virus, and apple chlorotic leafspot virus. More samples are currently being analysed. Assessing the viral status of old historical cultivars and original landraces maintained in these collections will also provide information to plant breeders about possible resistant or tolerant fruit tree cultivars.